Empowering grassroots innovation to accelerate biomedical research.

The purpose of biomedicine is to serve society, yet its hierarchical and closed structure excludes many citizens from the process of innovation. We propose a collection of reforms to better integrate citizens within the research community, reimagining biomedicine as more participatory, inclusive, and responsive to societal needs.

Ethical and social implications of approaching death prediction in humans - when the biology of ageing meets existential issues.

BACKGROUND: The discovery of biomarkers of ageing has led to the development of predictors of impending natural death and has paved the way for personalised estimation of the risk of death in the general population. This study intends to identify the ethical resources available to approach the idea of a long-lasting dying process and consider the perspective of death prediction. The reflection on human mortality is necessary but not sufficient to face this issue. Knowledge about death anticipation in clinical contexts allows for a better understanding of it. Still, the very notion of prediction and its implications must be clarified. This study outlines in a prospective way issues that call for further investigation in the various fields concerned: ethical, psychological, medical and social. METHODS: The study is based on an interdisciplinary approach, a combination of philosophy, clinical psychology, medicine, demography, biology and actuarial science. RESULTS: The present study proposes an understanding of death prediction based on its distinction with the relationship to human mortality and death anticipation, and on the analogy with the implications of genetic testing performed in pre-symptomatic stages of a disease. It leads to the identification of a multi-layered issue, including the individual and personal relationship to death prediction, the potential medical uses of biomarkers of ageing, the social and economic implications of the latter, especially in regard to the way longevity risk is perceived. CONCLUSIONS: The present study work strives to propose a first sketch of what the implications of death prediction as such could be - from an individual, medical and social point of view. Both with anti-ageing medicine and the transhumanist quest for immortality, research on biomarkers of ageing brings back to the forefront crucial ethical matters: should we, as human beings, keep ignoring certain things, primarily the moment of our death, be it an estimation of it? If such knowledge was available, who should be informed about it and how such information should be given? Is it a knowledge that could be socially shared?

A birth-death model of ageing: from individual-based dynamics to evolutive differential inclusions.

Ageing's sensitivity to natural selection has long been discussed because of its apparent negative effect on an individual's fitness. Thanks to the recently described (Smurf) 2-phase model of ageing (Tricoire and Rera in PLoS ONE 10(11):e0141920, 2015) we propose a fresh angle for modeling the evolution of ageing. Indeed, by coupling a dramatic loss of fertility with a high-risk of impending death-amongst other multiple so-called hallmarks of ageing-the Smurf phenotype allowed us to consider ageing as a couple of sharp transitions. The birth-death model (later called bd-model) we describe here is a simple life-history trait model where each asexual and haploid individual is described by its fertility period [Formula: see text] and survival period [Formula: see text]. We show that, thanks to the Lansing effect, the effect through which the "progeny of old parents do not live as long as those of young parents", [Formula: see text] and [Formula: see text] converge during evolution to configurations [Formula: see text] in finite time. To do so, we built an individual-based stochastic model which describes the age and trait distribution dynamics of such a finite population. Then we rigorously derive the adaptive dynamics models, which describe the trait dynamics at the evolutionary time-scale. We extend the Trait Substitution Sequence with age structure to take into account the Lansing effect. Finally, we study the limiting behaviour of this jump process when mutations are small. We show that the limiting behaviour is described by a differential inclusion whose solutions [Formula: see text] reach the diagonal [Formula: see text] in finite time and then remain on it. This differential inclusion is a natural way to extend the canonical equation of adaptive dynamics in order to take into account the lack of regularity of the invasion fitness function on the diagonal [Formula: see text].

The Smurf transition: new insights on ageing from end-of-life studies in animal models.

PURPOSE OF REVIEW: Over the past 5 years, many articles were published concerning the prediction of high risk of mortality in apparently healthy adults, echoing the first description in 2011 of the Smurf phenotype, a harbinger of natural death in drosophila. RECENT FINDINGS: These recent findings suggest that the end-of-life is molecularly and physiologically highly stereotyped, evolutionarily conserved and predictable. SUMMARY: Taken altogether, these results from independent teams using multiple organisms including humans draw the lines of future directions in ageing research. The ability to identify and study individuals about to die of natural causes with no apparent diseases is a game-changer in this field. In addition, the public health applications are potentially of tremendous impact in our ageing societies and raise important ethical questions.

Parkin overexpression during aging reduces proteotoxicity, alters mitochondrial dynamics, and extends lifespan.

Aberrant protein aggregation and mitochondrial dysfunction have each been linked to aging and a number of age-onset neurodegenerative disorders, including Parkinson disease. Loss-of-function mutations in parkin, an E3 ubiquitin ligase that functions to promote the ubiquitin-proteasome system of protein degradation and also in mitochondrial quality control, have been implicated in heritable forms of Parkinson disease. The question of whether parkin can modulate aging or positively impact longevity, however, has not been addressed. Here, we show that ubiquitous or neuron-specific up-regulation of Parkin, in adult Drosophila melanogaster, increases both mean and maximum lifespan without reducing reproductive output, physical activity, or food intake. Long-lived Parkin-overexpressing flies display an increase in K48-linked polyubiquitin and reduced levels of protein aggregation during aging. Recent evidence suggests that Parkin interacts with the mitochondrial fission/fusion machinery to mediate the turnover of dysfunctional mitochondria. However, the relationships between parkin gene activity, mitochondrial dynamics, and aging have not been explored. We show that the mitochondrial fusion-promoting factor Drosophila Mitofusin, a Parkin substrate, increases in abundance during aging. Parkin overexpression results in reduced Drosophila Mitofusin levels in aging flies, with concomitant changes in mitochondrial morphology and an increase in mitochondrial activity. Together, these findings reveal roles for Parkin in modulating organismal aging and provide insight into the molecular mechanisms linking aging to neurodegeneration.

Intestinal barrier dysfunction links metabolic and inflammatory markers of aging to death in Drosophila.

Aging is characterized by a growing risk of disease and death, yet the underlying pathophysiology is poorly understood. Indeed, little is known about how the functional decline of individual organ systems relates to the integrative physiology of aging and probability of death of the organism. Here we show that intestinal barrier dysfunction is correlated with lifespan across a range of Drosophila genotypes and environmental conditions, including mitochondrial dysfunction and dietary restriction. Regardless of chronological age, intestinal barrier dysfunction predicts impending death in individual flies. Activation of inflammatory pathways has been linked to aging and age-related diseases in humans, and an age-related increase in immunity-related gene expression has been reported in Drosophila. We show that the age-related increase in expression of antimicrobial peptides is tightly linked to intestinal barrier dysfunction. Indeed, increased antimicrobial peptide expression during aging can be used to identify individual flies exhibiting intestinal barrier dysfunction. Similarly, intestinal barrier dysfunction is more accurate than chronological age in identifying individual flies with systemic metabolic defects previously linked to aging, including impaired insulin/insulin-like growth factor signaling, as evidenced by a reduction in Akt activation and up-regulation of dFOXO target genes. Thus, the age-dependent loss of intestinal integrity is associated with altered metabolic and immune signaling and, critically, is a harbinger of death. Our findings suggest that intestinal barrier dysfunction may be an important factor in the pathophysiology of aging in other species as well, including humans.

dJun and Vri/dNFIL3 are major regulators of cardiac aging in Drosophila.

Cardiac aging is a complex process, which is influenced by both environmental and genetic factors. Deciphering the mechanisms involved in heart senescence therefore requires identifying the molecular pathways that are affected by age in controlled environmental and genetic conditions. We describe a functional genomic investigation of the genetic control of cardiac senescence in Drosophila. Molecular signatures of heart aging were identified by differential transcriptome analysis followed by a detailed bio-informatic analysis. This approach implicated the JNK/dJun pathway and the transcription factor Vri/dNFIL3 in the transcription regulatory network involved in cardiac senescence and suggested the possible involvement of oxidative stress (OS) in the aging process. To validate these predictions, we developed a new in vivo assay to analyze heart performance in various contexts of adult heart-specific gene overexpression and inactivation. We demonstrate that, as in mammals, OS plays a central role in cardiac senescence, and we show that pharmacological interventions impinging on OS slow heart senescence. These observations strengthen the idea that cardiac aging is controlled by evolutionarily conserved mechanisms, further validating Drosophila as a model to study cardiac senescence. In addition, we demonstrate that Vri, the ortholog of the vertebrate NFIL3/E4B4 transcription factor, is a major genetic regulator of cardiac aging. Vri overexpression leads to major heart dysfunctions, but its loss of function significantly reduces age-related cardiac dysfunctions. Furthermore, we unambiguously show that the JNK/AP1 pathway, the role of which in cardiac aging in mammals is controversial, is activated during cardiac aging and has a detrimental effect on cardiac senescence. This data-driven functional genomic analysis therefore led to the identification of key components of the Gene Regulatory Network of cardiac aging in Drosophila and may prompt to investigate the involvement of their counterparts in the cardiac aging process in mammals.

Ageing as a two-phase process: theoretical framework.

Human ageing, along with the ageing of conventional model organisms, is depicted as a continuous and progressive decline of biological capabilities accompanied by an exponentially increasing mortality risk. However, not all organisms experience ageing identically and our understanding of the phenomenon is coloured by human-centric views. Ageing is multifaceted and influences a diverse range of species in varying ways. Some undergo swift declines post-reproduction, while others exhibit insubstantial changes throughout their existence. This vast array renders defining universally applicable "ageing attributes" a daunting task. It is nonetheless essential to recognize that not all ageing features are organism-specific. These common attributes have paved the way for identifying "hallmarks of ageing," processes that are intertwined with age, amplified during accelerated ageing, and manipulations of which can potentially modulate or even reverse the ageing process. Yet, a glaring observation is that individuals within a single population age at varying rates. To address this, demographers have coined the term 'frailty'. Concurrently, scientific advancements have ushered in the era of molecular clocks. These innovations enable a distinction between an individual's chronological age (time since birth) and biological age (physiological status and mortality risk). In 2011, the "Smurf" phenotype was unveiled in Drosophila, delineating an age-linked escalation in intestinal permeability that presages imminent mortality. It not only acts as a predictor of natural death but identifies individuals exhibiting traits normally described as age-related. Subsequent studies have revealed the phenotype in organisms like nematodes, zebrafish, and mice, invariably acting as a death predictor. Collectively, these findings have steered our conception of ageing towards a framework where ageing is not linear and continuous but marked by two distinct, necessary phases, discernible in vivo, courtesy of the Smurf phenotype. This framework includes a mathematical enunciation of longevity trends based on three experimentally measurable parameters. It facilitates a fresh perspective on the evolution of ageing as a function. In this article, we aim to delineate and explore the foundational principles of this innovative framework, emphasising its potential to reshape our understanding of ageing, challenge its conventional definitions, and recalibrate our comprehension of its evolutionary trajectory.

Alignment-based Protein Mutational Landscape Prediction: Doing More with Less.

The wealth of genomic data has boosted the development of computational methods predicting the phenotypic outcomes of missense variants. The most accurate ones exploit multiple sequence alignments, which can be costly to generate. Recent efforts for democratizing protein structure prediction have overcome this bottleneck by leveraging the fast homology search of MMseqs2. Here, we show the usefulness of this strategy for mutational outcome prediction through a large-scale assessment of 1.5M missense variants across 72 protein families. Our study demonstrates the feasibility of producing alignment-based mutational landscape predictions that are both high-quality and compute-efficient for entire proteomes. We provide the community with the whole human proteome mutational landscape and simplified access to our predictive pipeline.

Drosophilids with darker cuticle have higher body temperature under light.

Cuticle pigmentation was shown to be associated with body temperature for several relatively large species of insects, but it was questioned for small insects. Here we used a thermal camera to assess the association between drosophilid cuticle pigmentation and body temperature increase when individuals are exposed to light. We compared mutants of large effects within species (Drosophila melanogaster ebony and yellow mutants). Then we analyzed the impact of naturally occurring pigmentation variation within species complexes (Drosophila americana/Drosophila novamexicana and Drosophila yakuba/Drosophila santomea). Finally we analyzed lines of D. melanogaster with moderate differences in pigmentation. We found significant differences in temperatures for each of the four pairs we analyzed. The temperature differences appeared to be proportional to the differently pigmented area: between Drosophila melanogaster ebony and yellow mutants or between Drosophila americana and Drosophila novamexicana, for which the whole body is differently pigmented, the temperature difference was around 0.6 °C ± 0.2 °C. By contrast, between D. yakuba and D. santomea or between Drosophila melanogaster Dark and Pale lines, for which only the posterior abdomen is differentially pigmented, we detected a temperature difference of about 0.14 °C ± 0.10 °C. This strongly suggests that cuticle pigmentation has ecological implications in drosophilids regarding adaptation to environmental temperature.

Intestinal barrier dysfunction: an evolutionarily conserved hallmark of aging.

A major challenge in the biology of aging is to understand how specific age-onset pathologies relate to the overall health of the organism. The integrity of the intestinal epithelium is essential for the wellbeing of the organism throughout life. In recent years, intestinal barrier dysfunction has emerged as an evolutionarily conserved feature of aged organisms, as reported in worms, flies, fish, rodents and primates. Moreover, age-onset intestinal barrier dysfunction has been linked to microbial alterations, elevated immune responses, metabolic alterations, systemic health decline and mortality. Here, we provide an overview of these findings. We discuss early work in the Drosophila model that sets the stage for examining the relationship between intestinal barrier integrity and systemic aging, then delve into research in other organisms. An emerging concept, supported by studies in both Drosophila and mice, is that directly targeting intestinal barrier integrity is sufficient to promote longevity. A better understanding of the causes and consequences of age-onset intestinal barrier dysfunction has significant relevance to the development of interventions to promote healthy aging.

Smurfness-based two-phase model of ageing helps deconvolve the ageing transcriptional signature.

Ageing is characterised at the molecular level by six transcriptional 'hallmarks of ageing', that are commonly described as progressively affected as time passes. By contrast, the 'Smurf' assay separates high-and-constant-mortality risk individuals from healthy, zero-mortality risk individuals, based on increased intestinal permeability. Performing whole body total RNA sequencing, we found that Smurfness distinguishes transcriptional changes associated with chronological age from those associated with biological age. We show that transcriptional heterogeneity increases with chronological age in non-Smurf individuals preceding the other five hallmarks of ageing that are specifically associated with the Smurf state. Using this approach, we also devise targeted pro-longevity genetic interventions delaying entry in the Smurf state. We anticipate that increased attention to the evolutionary conserved Smurf phenotype will bring about significant advances in our understanding of the mechanisms of ageing.

[Ethical and social consequences of biomarkers that predict impending death in humans]. / Conséquences éthiques et sociales de biomarqueurs prédictifs de la mort chez l'homme - La vieillesse et la mort, problématiques comportementales et sociétales.

Fundamental research on ageing has taken an interesting turn in recent years with the rapid development of biomarkers predicting mortality in model organisms, particularly Drosophila, as well as in humans through improvements in approaches to the identification of circulating molecules in mass. These developments lead to a shift in our ability to predict the occurrence of death from the historically population level to the individual level. We question here the ethical, medical and social implications of this change of scale.

TITLE: Conséquences éthiques et sociales de biomarqueurs prédictifs de la mort chez l'homme - La vieillesse et la mort, problématiques comportementales et sociétales. ABSTRACT: La recherche fondamentale sur le vieillissement a pris un tour intéressant ces dernières années avec un développement rapide des biomarqueurs prédictifs de mortalité chez les organismes modèles, notamment la drosophile, ainsi que chez l'être humain à travers les améliorations des approches d'identification en masse de molécules circulantes. Ces développements conduisent à un déplacement de notre capacité de prédiction de survenue de la mort, du niveau historiquement populationnel au niveau individuel. Nous interrogeons ici les implications éthiques, médicales et sociales de ce changement d'échelle.

Identification of cardioprotective drugs by medium-scale in vivo pharmacological screening on a Drosophila cardiac model of Friedreich's ataxia.

Friedreich's ataxia (FA) is caused by reduced levels of frataxin, a highly conserved mitochondrial protein. There is currently no effective treatment for this disease, which is characterized by progressive neurodegeneration and cardiomyopathy, the latter being the most common cause of death in patients. We previously developed a Drosophila melanogaster cardiac model of FA, in which the fly frataxin is inactivated specifically in the heart, leading to heart dilatation and impaired systolic function. Methylene Blue (MB) was highly efficient to prevent these cardiac dysfunctions. Here, we used this model to screen in vivo the Prestwick Chemical Library, comprising 1280 compounds. Eleven drugs significantly reduced the cardiac dilatation, some of which may possibly lead to therapeutic applications in the future. The one with the strongest protective effects was paclitaxel, a microtubule-stabilizing drug. In parallel, we characterized the histological defects induced by frataxin deficiency in cardiomyocytes and observed strong sarcomere alterations with loss of striation of actin fibers, along with full disruption of the microtubule network. Paclitaxel and MB both improved these structural defects. Therefore, we propose that frataxin inactivation induces cardiac dysfunction through impaired sarcomere assembly or renewal due to microtubule destabilization, without excluding additional mechanisms. This study is the first drug screening of this extent performed in vivo on a Drosophila model of cardiac disease. Thus, it also brings the proof of concept that cardiac functional imaging in adult Drosophila flies is usable for medium-scale in vivo pharmacological screening, with potent identification of cardioprotective drugs in various contexts of cardiac diseases.

How to Catch a Smurf? - Ageing and Beyond In vivo Assessment of Intestinal Permeability in Multiple Model Organisms.

The Smurf Assay (SA) was initially developed in the model organism Drosophila melanogaster where a dramatic increase of intestinal permeability has been shown to occur during aging (Rera et al., 2011). We have since validated the protocol in multiple other model organisms (Dambroise et al., 2016) and have utilized the assay to further our understanding of aging (Tricoire and Rera, 2015; Rera et al., 2018). The SA has now also been used by other labs to assess intestinal barrier permeability (Clark et al., 2015; Katzenberger et al., 2015; Barekat et al., 2016; Chakrabarti et al., 2016; Gelino et al., 2016). The SA in itself is simple; however, numerous small details can have a considerable impact on its experimental validity and subsequent interpretation. Here, we provide a detailed update on the SA technique and explain how to catch a Smurf while avoiding the most common experimental fallacies.

Promoting Drp1-mediated mitochondrial fission in midlife prolongs healthy lifespan of Drosophila melanogaster.

The accumulation of dysfunctional mitochondria has been implicated in aging, but a deeper understanding of mitochondrial dynamics and mitophagy during aging is missing. Here, we show that upregulating Drp1-a Dynamin-related protein that promotes mitochondrial fission-in midlife, prolongs Drosophila lifespan and healthspan. We find that short-term induction of Drp1, in midlife, is sufficient to improve organismal health and prolong lifespan, and observe a midlife shift toward a more elongated mitochondrial morphology, which is linked to the accumulation of dysfunctional mitochondria in aged flight muscle. Promoting Drp1-mediated mitochondrial fission, in midlife, facilitates mitophagy and improves both mitochondrial respiratory function and proteostasis in aged flies. Finally, we show that autophagy is required for the anti-aging effects of midlife Drp1-mediated mitochondrial fission. Our findings indicate that interventions that promote mitochondrial fission could delay the onset of pathology and mortality in mammals when applied in midlife.Mitochondrial fission and fusion are important mechanisms to maintain mitochondrial function. Here, the authors report that middle-aged flies have more elongated, or 'hyper-fused' mitochondria, and show that induction of mitochondrial fission in midlife, but not in early life, extends the health and life of flies.

A New, Discontinuous 2 Phases of Aging Model: Lessons from Drosophila melanogaster.

Aging is commonly described as being a continuous process affecting progressively organisms as time passes. This process results in a progressive decrease in individuals fitness through a wide range of both organismal-decreased motor activity, fertility, resistance to stress-and molecular phenotypes-decreased protein and energy homeostasis, impairment of insulin signaling. In the past 20 years, numerous genes have been identified as playing a major role in the aging process, yet little is known about the events leading to that loss of fitness. We recently described an event characterized by a dramatic increase of intestinal permeability to a blue food dye in aging flies committed to die within a few days. Importantly, flies showing this so called 'Smurf' phenotype are the only ones, among a population, to show various age-related changes and exhibit a high-risk of impending death whatever their chronological age. Thus, these observations suggest that instead of being one continuous phenomenon, aging may be a discontinuous process well described by at least two distinguishable phases. In this paper we addressed this hypothesis by implementing a new 2 Phases of Aging mathematiCal model (2PAC model) to simulate longevity curves based on the simple hypothesis of two consecutive phases of lifetime presenting different properties. We first present a unique equation for each phase and discuss the biological significance of the 3 associated parameters. Then we evaluate the influence of each parameter on the shape of survival curves. Overall, this new mathematical model, based on simple biological observations, is able to reproduce many experimental longevity curves, supporting the existence of 2 phases of aging exhibiting specific properties and separated by a dramatic transition that remains to be characterized. Moreover, it indicates that Smurf survival can be approximated by one single constant parameter for a broad range of genotypes that we have tested under our environmental conditions.

A Yeast/Drosophila Screen to Identify New Compounds Overcoming Frataxin Deficiency.

Friedreich's ataxia (FA) is a rare neurodegenerative disease which is very debilitating for the patients who progressively lose their autonomy. The lack of efficient therapeutic treatment of the disease strongly argues for urgent need to search for new active compounds that may stop the progression of the disease or prevent the appearance of the symptoms when the genetic defect is diagnosed early enough. In the present study, we used a yeast strain with a deletion of the frataxin homologue gene as a model of FA cells in a primary screen of two chemical libraries, a fraction of the French National Chemical Library (5500 compounds) and the Prestwick collection (880 compounds). We ran a secondary screen on Drosophila melanogaster flies expressing reduced levels of frataxin during larval development. Half of the compounds selected in yeast appeared to be active in flies in this developmental paradigm, and one of the two compounds with highest activities in this assay partially rescued the heart dilatation phenotype resulting from heart specific depletion of frataxin. The unique complementarity of these two frataxin-deficient models, unicellular and multicellular, appears to be very efficient to select new compounds with improved selectivity, bringing significant perspectives towards improvements in FA therapy.

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality.

Alterations in the composition of the intestinal microbiota have been correlated with aging and measures of frailty in the elderly. However, the relationships between microbial dynamics, age-related changes in intestinal physiology, and organismal health remain poorly understood. Here, we show that dysbiosis of the intestinal microbiota, characterized by an expansion of the Gammaproteobacteria, is tightly linked to age-onset intestinal barrier dysfunction in Drosophila. Indeed, alterations in the microbiota precede and predict the onset of intestinal barrier dysfunction in aged flies. Changes in microbial composition occurring prior to intestinal barrier dysfunction contribute to changes in excretory function and immune gene activation in the aging intestine. In addition, we show that a distinct shift in microbiota composition follows intestinal barrier dysfunction, leading to systemic immune activation and organismal death. Our results indicate that alterations in microbiota dynamics could contribute to and also predict varying rates of health decline during aging in mammals.